Trypsin revisited: crystallography AT (SUB) atomic resolution and quantum chemistry revealing details of catalysis

J Biol Chem. 2003 Oct 31;278(44):43357-62. doi: 10.1074/jbc.M306944200. Epub 2003 Aug 22.


A series of crystal structures of trypsin, containing either an autoproteolytic cleaved peptide fragment or a covalently bound inhibitor, were determined at atomic and ultra-high resolution and subjected to ab initio quantum chemical calculations and multipole refinement. Quantum chemical calculations reproduced the observed active site crystal structure with severe deviations from standard stereochemistry and indicated the protonation state of the catalytic residues. Multipole refinement directly revealed the charge distribution in the active site and proved the validity of the ab initio calculations. The combined results confirmed the catalytic function of the active site residues and the two water molecules acting as the nucleophile and the proton donor. The crystal structures represent snapshots from the reaction pathway, close to a tetrahedral intermediate. The de-acylation of trypsin then occurs in true SN2 fashion.

MeSH terms

  • Binding Sites
  • Catalytic Domain
  • Crystallography, X-Ray
  • Databases as Topic
  • Electrons
  • Freezing
  • Fusarium / chemistry
  • Models, Chemical
  • Models, Molecular
  • Peptides / chemistry
  • Phosphoric Triester Hydrolases / chemistry
  • Protease Inhibitors / pharmacology
  • Tosyl Compounds / pharmacology
  • Trypsin / chemistry*


  • Peptides
  • Protease Inhibitors
  • Tosyl Compounds
  • 4-toluenesulfonyl fluoride
  • Phosphoric Triester Hydrolases
  • diisopropyl-fluorophosphatase
  • Trypsin

Associated data

  • PDB/1PPZ
  • PDB/1PQ5
  • PDB/1PQ7
  • PDB/1PQ8
  • PDB/1PQA